Starting phenix.real_space_refine on Fri Aug 22 21:35:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c2a_45152/08_2025/9c2a_45152_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c2a_45152/08_2025/9c2a_45152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9c2a_45152/08_2025/9c2a_45152_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c2a_45152/08_2025/9c2a_45152_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9c2a_45152/08_2025/9c2a_45152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c2a_45152/08_2025/9c2a_45152.map" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 5058 2.51 5 N 1254 2.21 5 O 1479 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7833 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2437 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 295} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 112 Unusual residues: {'NAG': 3, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Restraints were copied for chains: B, C, E, F Time building chain proxies: 1.61, per 1000 atoms: 0.21 Number of scatterers: 7833 At special positions: 0 Unit cell: (85.6416, 87.588, 122.623, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1479 8.00 N 1254 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 217 " - pdb=" SG CYS A 227 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 270 " distance=2.03 Simple disulfide: pdb=" SG CYS B 217 " - pdb=" SG CYS B 227 " distance=2.03 Simple disulfide: pdb=" SG CYS C 217 " - pdb=" SG CYS C 227 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 270 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 270 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 401 " - " ASN A 242 " " NAG A 402 " - " ASN A 184 " " NAG A 403 " - " ASN A 300 " " NAG B 401 " - " ASN B 242 " " NAG B 402 " - " ASN B 184 " " NAG B 403 " - " ASN B 300 " " NAG C 401 " - " ASN C 242 " " NAG C 402 " - " ASN C 184 " " NAG C 403 " - " ASN C 300 " " NAG D 1 " - " ASN A 153 " " NAG E 1 " - " ASN B 153 " " NAG F 1 " - " ASN C 153 " Time building additional restraints: 0.47 Conformation dependent library (CDL) restraints added in 243.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 9 sheets defined 27.8% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 30 through 47 Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.836A pdb=" N GLU A 183 " --> pdb=" O ARG A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 242 through 249 removed outlier: 3.516A pdb=" N LYS A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 327 through 354 removed outlier: 3.770A pdb=" N THR A 331 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 47 Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 179 through 184 removed outlier: 3.836A pdb=" N GLU B 183 " --> pdb=" O ARG B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 199 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 242 through 249 removed outlier: 3.517A pdb=" N LYS B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 327 through 354 removed outlier: 3.770A pdb=" N THR B 331 " --> pdb=" O ASP B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 86 through 90 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 179 through 184 removed outlier: 3.836A pdb=" N GLU C 183 " --> pdb=" O ARG C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 199 Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 242 through 249 removed outlier: 3.516A pdb=" N LYS C 249 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 327 through 354 removed outlier: 3.769A pdb=" N THR C 331 " --> pdb=" O ASP C 327 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 56 through 59 current: chain 'A' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 99 through 118 current: chain 'A' and resid 144 through 151 removed outlier: 9.229A pdb=" N ILE A 144 " --> pdb=" O TRP A 164 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TRP A 164 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR A 146 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE A 162 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS A 148 " --> pdb=" O GLU A 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 157 through 165 current: chain 'A' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 273 through 277 current: chain 'A' and resid 302 through 326 Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 56 through 59 current: chain 'B' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 99 through 118 current: chain 'B' and resid 144 through 151 removed outlier: 9.229A pdb=" N ILE B 144 " --> pdb=" O TRP B 164 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N TRP B 164 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N THR B 146 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE B 162 " --> pdb=" O THR B 146 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N LYS B 148 " --> pdb=" O GLU B 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 157 through 165 current: chain 'B' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 273 through 277 current: chain 'B' and resid 302 through 326 Processing sheet with id=AA5, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA6, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AA7, first strand: chain 'C' and resid 56 through 59 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 56 through 59 current: chain 'C' and resid 99 through 118 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 99 through 118 current: chain 'C' and resid 144 through 151 removed outlier: 9.228A pdb=" N ILE C 144 " --> pdb=" O TRP C 164 " (cutoff:3.500A) removed outlier: 9.006A pdb=" N TRP C 164 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N THR C 146 " --> pdb=" O PHE C 162 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE C 162 " --> pdb=" O THR C 146 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N LYS C 148 " --> pdb=" O GLU C 160 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 157 through 165 current: chain 'C' and resid 273 through 277 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 273 through 277 current: chain 'C' and resid 302 through 326 Processing sheet with id=AA8, first strand: chain 'C' and resid 62 through 70 Processing sheet with id=AA9, first strand: chain 'C' and resid 73 through 74 211 hydrogen bonds defined for protein. 534 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.75 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1410 1.33 - 1.45: 2031 1.45 - 1.57: 4449 1.57 - 1.69: 0 1.69 - 1.81: 51 Bond restraints: 7941 Sorted by residual: bond pdb=" N ILE B 335 " pdb=" CA ILE B 335 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.96e+00 bond pdb=" N ILE A 335 " pdb=" CA ILE A 335 " ideal model delta sigma weight residual 1.460 1.498 -0.038 1.21e-02 6.83e+03 9.89e+00 bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.82e+00 bond pdb=" N VAL B 156 " pdb=" CA VAL B 156 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.82e+00 bond pdb=" N VAL C 156 " pdb=" CA VAL C 156 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.20e-02 6.94e+03 9.82e+00 ... (remaining 7936 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 9574 1.46 - 2.93: 1014 2.93 - 4.39: 196 4.39 - 5.85: 13 5.85 - 7.31: 6 Bond angle restraints: 10803 Sorted by residual: angle pdb=" C CYS A 117 " pdb=" CA CYS A 117 " pdb=" CB CYS A 117 " ideal model delta sigma weight residual 111.17 103.86 7.31 1.96e+00 2.60e-01 1.39e+01 angle pdb=" C CYS C 117 " pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " ideal model delta sigma weight residual 111.17 103.88 7.29 1.96e+00 2.60e-01 1.38e+01 angle pdb=" C CYS B 117 " pdb=" CA CYS B 117 " pdb=" CB CYS B 117 " ideal model delta sigma weight residual 111.17 103.92 7.25 1.96e+00 2.60e-01 1.37e+01 angle pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" O VAL A 40 " ideal model delta sigma weight residual 121.17 117.27 3.90 1.06e+00 8.90e-01 1.35e+01 angle pdb=" CA VAL C 40 " pdb=" C VAL C 40 " pdb=" O VAL C 40 " ideal model delta sigma weight residual 121.17 117.28 3.89 1.06e+00 8.90e-01 1.34e+01 ... (remaining 10798 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 4698 17.42 - 34.84: 276 34.84 - 52.26: 81 52.26 - 69.68: 24 69.68 - 87.09: 9 Dihedral angle restraints: 5088 sinusoidal: 2460 harmonic: 2628 Sorted by residual: dihedral pdb=" CB CYS C 217 " pdb=" SG CYS C 217 " pdb=" SG CYS C 227 " pdb=" CB CYS C 227 " ideal model delta sinusoidal sigma weight residual 93.00 178.30 -85.30 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS B 217 " pdb=" SG CYS B 217 " pdb=" SG CYS B 227 " pdb=" CB CYS B 227 " ideal model delta sinusoidal sigma weight residual 93.00 178.28 -85.28 1 1.00e+01 1.00e-02 8.81e+01 dihedral pdb=" CB CYS A 217 " pdb=" SG CYS A 217 " pdb=" SG CYS A 227 " pdb=" CB CYS A 227 " ideal model delta sinusoidal sigma weight residual 93.00 178.27 -85.27 1 1.00e+01 1.00e-02 8.81e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 801 0.047 - 0.094: 271 0.094 - 0.142: 149 0.142 - 0.189: 33 0.189 - 0.236: 3 Chirality restraints: 1257 Sorted by residual: chirality pdb=" CA CYS A 117 " pdb=" N CYS A 117 " pdb=" C CYS A 117 " pdb=" CB CYS A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA CYS B 117 " pdb=" N CYS B 117 " pdb=" C CYS B 117 " pdb=" CB CYS B 117 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA CYS C 117 " pdb=" N CYS C 117 " pdb=" C CYS C 117 " pdb=" CB CYS C 117 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 1254 not shown) Planarity restraints: 1332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN B 37 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C GLN B 37 " 0.047 2.00e-02 2.50e+03 pdb=" O GLN B 37 " -0.018 2.00e-02 2.50e+03 pdb=" N LEU B 38 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN C 37 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C GLN C 37 " 0.046 2.00e-02 2.50e+03 pdb=" O GLN C 37 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU C 38 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 37 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.07e+00 pdb=" C GLN A 37 " -0.046 2.00e-02 2.50e+03 pdb=" O GLN A 37 " 0.017 2.00e-02 2.50e+03 pdb=" N LEU A 38 " 0.015 2.00e-02 2.50e+03 ... (remaining 1329 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 894 2.75 - 3.28: 7280 3.28 - 3.82: 12534 3.82 - 4.36: 16587 4.36 - 4.90: 27461 Nonbonded interactions: 64756 Sorted by model distance: nonbonded pdb=" O3 NAG C 401 " pdb=" O7 NAG C 401 " model vdw 2.207 3.040 nonbonded pdb=" O3 NAG B 401 " pdb=" O7 NAG B 401 " model vdw 2.208 3.040 nonbonded pdb=" O3 NAG A 401 " pdb=" O7 NAG A 401 " model vdw 2.208 3.040 nonbonded pdb=" O THR C 75 " pdb=" OG1 THR C 75 " model vdw 2.411 3.040 nonbonded pdb=" O THR A 75 " pdb=" OG1 THR A 75 " model vdw 2.411 3.040 ... (remaining 64751 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 6.230 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.047 7962 Z= 0.503 Angle : 0.946 7.315 10860 Z= 0.652 Chirality : 0.061 0.236 1257 Planarity : 0.008 0.098 1320 Dihedral : 12.743 87.094 3390 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.27), residues: 915 helix: -1.70 (0.28), residues: 270 sheet: 0.36 (0.30), residues: 276 loop : -0.76 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 314 TYR 0.011 0.001 TYR B 90 PHE 0.021 0.002 PHE A 293 TRP 0.021 0.002 TRP A 259 HIS 0.004 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00841 ( 7941) covalent geometry : angle 0.94423 (10803) SS BOND : bond 0.00424 ( 6) SS BOND : angle 1.51380 ( 12) hydrogen bonds : bond 0.17974 ( 211) hydrogen bonds : angle 7.16002 ( 534) link_BETA1-4 : bond 0.00271 ( 3) link_BETA1-4 : angle 0.95180 ( 9) link_NAG-ASN : bond 0.00150 ( 12) link_NAG-ASN : angle 1.21655 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.281 Fit side-chains REVERT: A 68 LYS cc_start: 0.7925 (ttmm) cc_final: 0.7725 (ttmt) REVERT: A 202 ARG cc_start: 0.8482 (mmm160) cc_final: 0.8145 (mmm160) REVERT: A 268 ARG cc_start: 0.7750 (ptm-80) cc_final: 0.7392 (ptm160) REVERT: B 188 PHE cc_start: 0.8511 (t80) cc_final: 0.8285 (t80) outliers start: 0 outliers final: 1 residues processed: 158 average time/residue: 0.5007 time to fit residues: 83.4971 Evaluate side-chains 150 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 273 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 114 GLN B 105 ASN C 105 ASN C 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.145229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.120256 restraints weight = 9924.230| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.34 r_work: 0.3336 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 7962 Z= 0.192 Angle : 0.555 4.847 10860 Z= 0.289 Chirality : 0.046 0.238 1257 Planarity : 0.004 0.038 1320 Dihedral : 8.560 58.020 1730 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.03 % Allowed : 9.47 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.28), residues: 915 helix: -0.07 (0.35), residues: 252 sheet: 0.68 (0.28), residues: 285 loop : -0.22 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.017 0.002 TYR A 90 PHE 0.013 0.002 PHE B 243 TRP 0.015 0.002 TRP A 259 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 7941) covalent geometry : angle 0.54978 (10803) SS BOND : bond 0.00540 ( 6) SS BOND : angle 0.97371 ( 12) hydrogen bonds : bond 0.04030 ( 211) hydrogen bonds : angle 4.94549 ( 534) link_BETA1-4 : bond 0.00540 ( 3) link_BETA1-4 : angle 0.72019 ( 9) link_NAG-ASN : bond 0.00247 ( 12) link_NAG-ASN : angle 1.34110 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.233 Fit side-chains REVERT: A 36 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.8013 (tp) REVERT: A 219 PHE cc_start: 0.8598 (t80) cc_final: 0.8291 (t80) REVERT: A 268 ARG cc_start: 0.8224 (ptm-80) cc_final: 0.7834 (ptm160) REVERT: B 114 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8366 (mt0) REVERT: B 188 PHE cc_start: 0.8752 (t80) cc_final: 0.8510 (t80) REVERT: B 268 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7869 (ptm160) outliers start: 24 outliers final: 8 residues processed: 160 average time/residue: 0.5311 time to fit residues: 89.7091 Evaluate side-chains 155 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 88 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 90 optimal weight: 0.0070 chunk 33 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 114 GLN B 120 HIS C 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.120891 restraints weight = 9889.960| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.34 r_work: 0.3337 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 7962 Z= 0.134 Angle : 0.490 4.808 10860 Z= 0.256 Chirality : 0.044 0.208 1257 Planarity : 0.004 0.042 1320 Dihedral : 8.471 59.873 1728 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.78 % Allowed : 12.12 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.28), residues: 915 helix: 0.18 (0.35), residues: 258 sheet: 0.84 (0.29), residues: 285 loop : -0.20 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 202 TYR 0.014 0.002 TYR A 90 PHE 0.022 0.001 PHE B 342 TRP 0.012 0.001 TRP A 259 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7941) covalent geometry : angle 0.48429 (10803) SS BOND : bond 0.00360 ( 6) SS BOND : angle 0.78591 ( 12) hydrogen bonds : bond 0.03359 ( 211) hydrogen bonds : angle 4.63552 ( 534) link_BETA1-4 : bond 0.00445 ( 3) link_BETA1-4 : angle 0.82069 ( 9) link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 1.24399 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7916 (tp) REVERT: A 219 PHE cc_start: 0.8614 (t80) cc_final: 0.8329 (t80) REVERT: A 275 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7855 (tt0) REVERT: B 114 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8335 (mt0) REVERT: B 268 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7830 (ptm160) outliers start: 22 outliers final: 13 residues processed: 163 average time/residue: 0.5246 time to fit residues: 90.1815 Evaluate side-chains 162 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 64 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 0.0980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 114 GLN B 120 HIS C 105 ASN C 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.144981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.119940 restraints weight = 10159.475| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3322 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 7962 Z= 0.176 Angle : 0.506 4.895 10860 Z= 0.263 Chirality : 0.045 0.211 1257 Planarity : 0.004 0.045 1320 Dihedral : 8.488 59.937 1728 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.91 % Allowed : 13.13 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.36 (0.28), residues: 915 helix: 0.26 (0.35), residues: 252 sheet: 0.85 (0.29), residues: 303 loop : -0.17 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 145 TYR 0.013 0.002 TYR A 90 PHE 0.018 0.002 PHE B 342 TRP 0.012 0.002 TRP A 259 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 7941) covalent geometry : angle 0.50016 (10803) SS BOND : bond 0.00513 ( 6) SS BOND : angle 0.94898 ( 12) hydrogen bonds : bond 0.03452 ( 211) hydrogen bonds : angle 4.60699 ( 534) link_BETA1-4 : bond 0.00363 ( 3) link_BETA1-4 : angle 0.80609 ( 9) link_NAG-ASN : bond 0.00235 ( 12) link_NAG-ASN : angle 1.28545 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 147 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7913 (tp) REVERT: B 114 GLN cc_start: 0.8600 (OUTLIER) cc_final: 0.8352 (mt0) REVERT: B 188 PHE cc_start: 0.8755 (t80) cc_final: 0.8511 (t80) REVERT: B 268 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7858 (ptm160) outliers start: 31 outliers final: 17 residues processed: 159 average time/residue: 0.5182 time to fit residues: 86.8121 Evaluate side-chains 165 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 61 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 120 HIS C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.144739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.119754 restraints weight = 10086.400| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 2.37 r_work: 0.3323 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7962 Z= 0.172 Angle : 0.498 4.871 10860 Z= 0.260 Chirality : 0.045 0.209 1257 Planarity : 0.004 0.044 1320 Dihedral : 8.380 59.998 1728 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.16 % Allowed : 15.15 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.38 (0.28), residues: 915 helix: 0.35 (0.35), residues: 252 sheet: 0.89 (0.30), residues: 285 loop : -0.18 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.014 0.002 TYR A 90 PHE 0.017 0.002 PHE B 342 TRP 0.012 0.002 TRP A 259 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 7941) covalent geometry : angle 0.49210 (10803) SS BOND : bond 0.00442 ( 6) SS BOND : angle 0.76684 ( 12) hydrogen bonds : bond 0.03396 ( 211) hydrogen bonds : angle 4.60468 ( 534) link_BETA1-4 : bond 0.00319 ( 3) link_BETA1-4 : angle 0.81190 ( 9) link_NAG-ASN : bond 0.00227 ( 12) link_NAG-ASN : angle 1.29101 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 147 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 36 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7896 (tp) REVERT: A 219 PHE cc_start: 0.8513 (t80) cc_final: 0.8293 (t80) REVERT: B 114 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: B 188 PHE cc_start: 0.8756 (t80) cc_final: 0.8508 (t80) REVERT: B 268 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7872 (ptm160) outliers start: 25 outliers final: 18 residues processed: 155 average time/residue: 0.5781 time to fit residues: 94.5036 Evaluate side-chains 168 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 273 ILE Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 103 MET Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.2980 chunk 69 optimal weight: 0.3980 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 120 HIS C 105 ASN C 120 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.144933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.120163 restraints weight = 10028.209| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.35 r_work: 0.3326 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 7962 Z= 0.153 Angle : 0.482 4.898 10860 Z= 0.251 Chirality : 0.044 0.204 1257 Planarity : 0.003 0.044 1320 Dihedral : 8.060 59.211 1728 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.54 % Allowed : 15.40 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.28), residues: 915 helix: 0.69 (0.36), residues: 240 sheet: 0.90 (0.28), residues: 330 loop : -0.36 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 145 TYR 0.014 0.001 TYR A 90 PHE 0.016 0.002 PHE B 342 TRP 0.010 0.002 TRP A 259 HIS 0.004 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 7941) covalent geometry : angle 0.47599 (10803) SS BOND : bond 0.00346 ( 6) SS BOND : angle 0.62251 ( 12) hydrogen bonds : bond 0.03181 ( 211) hydrogen bonds : angle 4.51000 ( 534) link_BETA1-4 : bond 0.00389 ( 3) link_BETA1-4 : angle 0.88369 ( 9) link_NAG-ASN : bond 0.00240 ( 12) link_NAG-ASN : angle 1.30273 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.318 Fit side-chains REVERT: A 36 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7852 (tp) REVERT: A 219 PHE cc_start: 0.8545 (t80) cc_final: 0.8318 (t80) REVERT: A 268 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7632 (ptm160) REVERT: B 114 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8339 (mt0) REVERT: B 144 ILE cc_start: 0.8757 (mt) cc_final: 0.8519 (mm) REVERT: B 188 PHE cc_start: 0.8750 (t80) cc_final: 0.8478 (t80) REVERT: B 268 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7864 (ptm160) REVERT: B 275 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7786 (tt0) REVERT: B 292 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8440 (mtm180) outliers start: 28 outliers final: 17 residues processed: 161 average time/residue: 0.6307 time to fit residues: 107.1352 Evaluate side-chains 171 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 4 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 chunk 76 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.2512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 105 ASN B 120 HIS C 120 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.145872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121019 restraints weight = 10064.231| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.37 r_work: 0.3345 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 7962 Z= 0.102 Angle : 0.453 4.922 10860 Z= 0.236 Chirality : 0.043 0.197 1257 Planarity : 0.003 0.042 1320 Dihedral : 7.763 59.600 1728 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.03 % Allowed : 16.67 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.29), residues: 915 helix: 0.87 (0.36), residues: 240 sheet: 0.98 (0.29), residues: 330 loop : -0.29 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.014 0.001 TYR A 90 PHE 0.014 0.001 PHE B 342 TRP 0.009 0.001 TRP C 259 HIS 0.004 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 7941) covalent geometry : angle 0.44618 (10803) SS BOND : bond 0.00379 ( 6) SS BOND : angle 1.11639 ( 12) hydrogen bonds : bond 0.02855 ( 211) hydrogen bonds : angle 4.41528 ( 534) link_BETA1-4 : bond 0.00374 ( 3) link_BETA1-4 : angle 0.92925 ( 9) link_NAG-ASN : bond 0.00298 ( 12) link_NAG-ASN : angle 1.25247 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.316 Fit side-chains REVERT: A 36 ILE cc_start: 0.8023 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 268 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7625 (ptm160) REVERT: A 292 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7870 (mtm180) REVERT: B 144 ILE cc_start: 0.8750 (mt) cc_final: 0.8533 (mm) REVERT: B 188 PHE cc_start: 0.8748 (t80) cc_final: 0.8484 (t80) REVERT: B 275 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7794 (tt0) outliers start: 24 outliers final: 14 residues processed: 163 average time/residue: 0.6291 time to fit residues: 108.2267 Evaluate side-chains 167 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.144520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.119635 restraints weight = 9970.524| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.35 r_work: 0.3316 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7962 Z= 0.190 Angle : 0.501 4.924 10860 Z= 0.261 Chirality : 0.045 0.203 1257 Planarity : 0.003 0.044 1320 Dihedral : 7.715 59.843 1728 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.28), residues: 915 helix: 0.86 (0.37), residues: 234 sheet: 0.95 (0.28), residues: 330 loop : -0.38 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.014 0.002 TYR A 90 PHE 0.018 0.002 PHE B 342 TRP 0.011 0.002 TRP A 259 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 7941) covalent geometry : angle 0.49421 (10803) SS BOND : bond 0.00542 ( 6) SS BOND : angle 1.09742 ( 12) hydrogen bonds : bond 0.03446 ( 211) hydrogen bonds : angle 4.58001 ( 534) link_BETA1-4 : bond 0.00405 ( 3) link_BETA1-4 : angle 0.90229 ( 9) link_NAG-ASN : bond 0.00217 ( 12) link_NAG-ASN : angle 1.35972 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.313 Fit side-chains REVERT: A 36 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7800 (tp) REVERT: A 219 PHE cc_start: 0.8506 (t80) cc_final: 0.8272 (t80) REVERT: A 268 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7623 (ptm160) REVERT: A 292 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8181 (mtm180) REVERT: B 144 ILE cc_start: 0.8729 (mt) cc_final: 0.8493 (mm) REVERT: B 188 PHE cc_start: 0.8765 (t80) cc_final: 0.8481 (t80) REVERT: B 275 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7797 (tt0) outliers start: 24 outliers final: 17 residues processed: 157 average time/residue: 0.6247 time to fit residues: 103.5562 Evaluate side-chains 167 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 147 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 111 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 6 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 4 optimal weight: 0.0050 chunk 20 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 120 HIS C 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.143766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.119177 restraints weight = 9862.001| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.33 r_work: 0.3316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7962 Z= 0.149 Angle : 0.477 4.962 10860 Z= 0.250 Chirality : 0.044 0.199 1257 Planarity : 0.003 0.044 1320 Dihedral : 7.510 59.794 1728 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.03 % Allowed : 17.42 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.29), residues: 915 helix: 0.82 (0.36), residues: 240 sheet: 0.97 (0.29), residues: 330 loop : -0.35 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 145 TYR 0.014 0.001 TYR A 90 PHE 0.016 0.001 PHE B 342 TRP 0.010 0.002 TRP B 259 HIS 0.005 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7941) covalent geometry : angle 0.46970 (10803) SS BOND : bond 0.00486 ( 6) SS BOND : angle 1.00874 ( 12) hydrogen bonds : bond 0.03156 ( 211) hydrogen bonds : angle 4.52710 ( 534) link_BETA1-4 : bond 0.00377 ( 3) link_BETA1-4 : angle 0.91779 ( 9) link_NAG-ASN : bond 0.00228 ( 12) link_NAG-ASN : angle 1.33933 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.338 Fit side-chains REVERT: A 36 ILE cc_start: 0.8011 (OUTLIER) cc_final: 0.7801 (tp) REVERT: A 219 PHE cc_start: 0.8526 (t80) cc_final: 0.8303 (t80) REVERT: A 268 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7632 (ptm160) REVERT: A 292 ARG cc_start: 0.8572 (OUTLIER) cc_final: 0.8128 (mtm180) REVERT: B 144 ILE cc_start: 0.8737 (mt) cc_final: 0.8522 (mm) REVERT: B 188 PHE cc_start: 0.8756 (t80) cc_final: 0.8483 (t80) REVERT: B 275 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7823 (tt0) outliers start: 24 outliers final: 16 residues processed: 162 average time/residue: 0.6189 time to fit residues: 106.0250 Evaluate side-chains 171 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 47 optimal weight: 0.2980 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.0770 chunk 92 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 105 ASN B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.144311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119775 restraints weight = 9888.620| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.34 r_work: 0.3325 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 7962 Z= 0.113 Angle : 0.454 4.905 10860 Z= 0.238 Chirality : 0.043 0.194 1257 Planarity : 0.003 0.043 1320 Dihedral : 7.317 59.383 1728 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.03 % Allowed : 17.68 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.29), residues: 915 helix: 0.95 (0.36), residues: 240 sheet: 1.01 (0.29), residues: 330 loop : -0.29 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 145 TYR 0.014 0.001 TYR A 90 PHE 0.015 0.001 PHE B 342 TRP 0.011 0.001 TRP C 85 HIS 0.005 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 7941) covalent geometry : angle 0.44688 (10803) SS BOND : bond 0.00367 ( 6) SS BOND : angle 0.86758 ( 12) hydrogen bonds : bond 0.02910 ( 211) hydrogen bonds : angle 4.42104 ( 534) link_BETA1-4 : bond 0.00374 ( 3) link_BETA1-4 : angle 0.95376 ( 9) link_NAG-ASN : bond 0.00273 ( 12) link_NAG-ASN : angle 1.28553 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1830 Ramachandran restraints generated. 915 Oldfield, 0 Emsley, 915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.301 Fit side-chains REVERT: A 36 ILE cc_start: 0.7955 (OUTLIER) cc_final: 0.7751 (tp) REVERT: A 219 PHE cc_start: 0.8526 (t80) cc_final: 0.8306 (t80) REVERT: A 268 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7622 (ptm160) REVERT: A 292 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.8028 (mtm180) REVERT: B 144 ILE cc_start: 0.8744 (mt) cc_final: 0.8537 (mm) REVERT: B 188 PHE cc_start: 0.8756 (t80) cc_final: 0.8491 (t80) REVERT: B 275 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7830 (tt0) outliers start: 24 outliers final: 15 residues processed: 163 average time/residue: 0.6311 time to fit residues: 108.6285 Evaluate side-chains 168 residues out of total 801 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 57 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 268 ARG Chi-restraints excluded: chain A residue 292 ARG Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain B residue 41 LEU Chi-restraints excluded: chain B residue 62 ILE Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 227 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain C residue 114 GLN Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 158 THR Chi-restraints excluded: chain C residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 21 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 0.0670 chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN A 120 HIS B 120 HIS C 105 ASN C 120 HIS C 290 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.143203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118466 restraints weight = 9908.328| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.34 r_work: 0.3305 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 7962 Z= 0.166 Angle : 0.485 5.010 10860 Z= 0.254 Chirality : 0.044 0.198 1257 Planarity : 0.003 0.045 1320 Dihedral : 7.314 59.073 1728 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.03 % Allowed : 17.93 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 21.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.29), residues: 915 helix: 1.00 (0.37), residues: 234 sheet: 0.98 (0.29), residues: 330 loop : -0.31 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 145 TYR 0.014 0.002 TYR A 90 PHE 0.018 0.002 PHE B 342 TRP 0.011 0.002 TRP B 259 HIS 0.005 0.001 HIS C 120 Details of bonding type rmsd covalent geometry : bond 0.00409 ( 7941) covalent geometry : angle 0.47842 (10803) SS BOND : bond 0.00492 ( 6) SS BOND : angle 0.91531 ( 12) hydrogen bonds : bond 0.03339 ( 211) hydrogen bonds : angle 4.53260 ( 534) link_BETA1-4 : bond 0.00368 ( 3) link_BETA1-4 : angle 0.93025 ( 9) link_NAG-ASN : bond 0.00230 ( 12) link_NAG-ASN : angle 1.34593 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3240.34 seconds wall clock time: 55 minutes 59.40 seconds (3359.40 seconds total)